Cellular differentiation is controlled, in part, by regulation of gene expression. Regulation of transcription; i.e., use of DNA as a template for the synthesis of a mRNA molecule; is one of the mechanisms by which gene expression is regulated. Transcriptional regulation of gene expression can result, for example, from alteration of chromatin structure and/or binding of transcriptional regulatory proteins to specific DNA sequences in or near the gene.
Another means by which transcriptional control of gene expression is effected is by chemical alteration of DNA. The most widely-studied aspect of this form of regulation is DNA methylation. In eukaryotic genomes, the primary form of DNA methylation is the conversion of cytosine to 5-methyl-cytosine, through the action of one of a number of cellular methyltransferases. In most cases, methylated C residues are located directly upstream of a G residue. In general, methylation of C residues in or near a gene is correlated with reduced expression of the gene. In most cases, CpG methylation is not itself the proximate cause of transcriptional repression of a gene, but appears to be a mechanism to perpetuate transcriptional repression initially mediated by gene regulatory proteins.
The frequency of CG dinucleotide sequences in the upstream regions of certain non-cell-type-specific vertebrate genes (i.e., housekeeping genes) is much higher than would be expected based on the GC content of the genome; such regions are known as CpG Islands. CpG Islands are sites at which the methylation state of the C residues can affect transcription of the associated gene. Conversely, the methylation state of C residues in a CpG island or other region associated with a particular gene can be used as a potential indicator of the transcriptional state of that gene and/or as a diagnostic marker to characterize a particular cell type. See, for example, WO 2006/094836.